UVR-absorbing mycosporine-like amino acids (MAAs) were detected in tissues of Strongylocentrotus purpuratus and in ten species of Rhodophyte macroalgae (eight previously untested) collected from intertidal microhabitats in November and January 2006–2007 in Central California (35°09'N, 120°45'W). In sea urchins, MAA concentrations were higher in ovaries than testes, while epidermal concentrations were similar between sexes. Ovaries and epidermal tissues had similar MAA signatures and broadband UVA/UVB absorbance, while testes had a narrower absorption ranges shifted toward higher energy wavelengths. Sea urchins occupying pits in the substrate exhibited lower MAA concentrations than those outside pits, suggesting adult microhabitat may impact UV protection. Light levels did not influence gonadal MAA concentrations, but correlated with elevated epidermal MAA concentrations for males in the sunniest microhabitat. This study suggests sex and habitat strongly influence MAA concentrations among individual S. purpuratus and that allocation of MAA sunscreens to tissues in response to UVR is sex-dependent.